Why it’s so hard to ramp up testing in Ontario
Boosting province’s lab capacity required a ‘herculean’ effort — yet it still may not be enough
Perhaps at no time in Ontario’s history has a five-digit data point been the focus of so much scrutiny, dispute, congratulation and anguish.
That data point is the number of COVID-19 tests completed in the past 24 hours. On days when it rises towards the province’s target of 20,000, officials celebrate. On days when it dives down towards 10,000, reporters and politicians demand answers — even as the cause of these fluctuations remains obscure.
“Start picking up your socks and start doing testing. I don’t know what the big problem is,” Premier Doug Ford said earlier this month, blaming public health officials after a reported 24hour tally of just 10,654.
Though the daily number oscillates, Ontario’s average has risen steadily from about 8,700 tests per day in the middle of April to 15,800 over the last week. That near-doubling was the result of a “herculean” effort from both public health units — a maxed-out workforce tasked with testing every long-term-care resident and worker in the province — and unprecedented expansion in the province’s laboratories.
Ontario has clawed its way to its current testing totals. And yet, it may not be enough. The province confirms it is still pushing to increase capacity; experts have floated goals of100,000 daily tests. Reopening the economy safely depends on having a near-omniscient view of the spread of the disease, to stamp out COVID-19 embers before they become wildfires.
That today’s hard-fought targets could be both an enormous achievement and still not enough demonstrates the formidable challenge ahead — although epidemiologists say it’s more important to test wisely than to hit some arbitrary number.
“It is an unbelievable leap, to have gotten to where we are and to be as successful as it is in a very short time,” said Dr. Larissa Matukas, head of microbiology at St. Michael’s Hospital, one of the hospital-based labs in the provincial network.
At the outbreak’s outset, Public Health Ontario was responsible for all testing. But by March, PHO’s lab was swamped by an enormous surge in demand. Dr. Vanessa Allen, chief of medical microbiology at PHO, co-ordinated with labs across the province to clear the backlog by early April. Allen now leads a formalized, integrated lab network, combining the resources of Ontario’s hospital, private and public health laboratories.
Yet even those combined resources were not enough. Individual labs in the network have each dramatically expanded their own capacity too, in some cases 20-fold over typical flu season volumes. Scientists who run these facilities have leveraged international research relationships to acquire cuttingedge equipment, validated more efficient processing methods in a fraction of the usual time, and even relied on colleagues graciously giving up their adjacent office space to grow labs’ physical footprints.
“It’s like, ‘Oh great, I have all this equipment … oh my gosh, where am I supposed to put it now?’ And it’s not just space — it’s the whole infrastructure, right? This is big machinery … it’s heavy, so it needs special benches. It needs maybe special electrical, all of the engineering side and planning side,” says Matukas, adding that space is at a premium in downtown Toronto hospitals.
Lab leaders juggle a headspinning list of pros and cons as they work to obtain new equipment. One instrument might be incredibly efficient at processing high volumes of tests, but rely on proprietary chemistry that is rationed by the manufacturer to supply all its global customers. Another instrument may be a better match for the lab’s pre-existing technology, but require highly skilled technicians to keep it running, a limited staffing pool. All of these instruments likely come from countries battling their own COVID-19 epidemics, leaving Canadian scientists wary of becoming too reliant on a single overseas manufacturer that may be pressured to prioritize domestic needs.
In the end, the labs are choosing to diversify.
“Rather than put all our eggs in one basket … we’re doing three different manufacturers’ tests, in the hopes that if one manufacturer goes down or can’t supply, we still have the other ones to back us up,” said Dr. Tony Mazzulli, microbiologist-in-chief at Sinai Health System.
Mount Sinai has the highestvolume hospital-based lab in Ontario’s network. Before the pandemic, the lab processed about 500 flu tests a day. Its capacity was boosted to about 3,400 COVID-19 tests daily, but starting this week, a trio of new instruments will begin pushing capacity towards 10,000 — although labs avoid running at full capacity 24-7, since any additional surge risks creating new, dangerous backlogs.
Sinai uses instrumentation from Luminex, a Texas-based company; Altona, a German company; and Seegene, a Korean company. Luminex is the fastest, providing results in under two hours, while the Seegene has been Sinai’s workhorse, processing just under 700 tests a day: the lab acquired Seegene’s technology after watching South Korea smother its outbreak early on, assuming one element of the country’s success was highly sensitive testing equipment.
Recently, Mazzulli’s lab connected with BGI Group, a nextgeneration genome sequencing company from China. Another Sinai scientist had a research relationship with the company and through that connection, Sinai acquired three new instruments that can each process 2,300 tests daily, once the lab optimizes workflow. The company has promised a steady flow of the supplies necessary to run the machines — even though Chinese officials recently declared they would test all 11 million residents of Wuhan, where a new case cluster was identified.
The work doesn’t end with finding equipment, space to put it and adequate staff, however. Every time a change is made, the process has to be “validated” all over again — a quality control check to make sure results are still accurate.
Swabs have been a massive challenge. Ideally, patients are swabbed with a long, thin nasopharyngeal swab, which is inserted deep into the nostril. One of the primary suppliers for these swabs is in northern
Italy, a region devastated by the pandemic. There are global shortages of the swabs.
Ontario started using swabs designed for testing sexually transmitted infections. They are too rigid to be inserted deep in the nose, however. The labs determined that swiping the inner nostril and throat with one STI swab gave accurate results, but that approach had to be validated. A new batch of Chinesemade nasopharyngeal swabs just arrived at Sinai; that too had to be validated. Sinai’s and Toronto Western Hospital’s assessment centres are now collecting saliva samples alongside typical samples, to see if this swab-free approach produces similarly accurate results.
The labs have increased efficiency through automation. But public health units that are responsible for collecting patient samples can’t automate their work: there is no robot that can insert a swab deep into the nostril of an 85-year-old long-term-care resident.
When the province put out a call to test every single resident and staff member in every longterm-care home across Ontario, public health units had already been working flat-out for weeks. They are also responsible for tracing the contacts of anyone who tests positive, without which testing is a fruitless exercise. They inspect workplaces and care homes for infection prevention strategies to stop outbreaks from happening in the first place.
“It was a herculean effort to do this,” said Dr. Julie Emili, the acting associate medical officer of health for Waterloo Region.
As with the labs, a test is never just a test. Before anyone is swabbed, requisitions and labels have to be organized so that the result can be matched to the patient. The health units scheduled their visits to accommodate multiple staff shifts and to make sure their local labs wouldn’t be swamped by a sudden surge. To actually carry out testing, they partnered with paramedics, family doctors, hospitals and more.
It was “truly a challenge for all of us,” said Dr. Wajid Ahmed, associate medical officer of health for Windsor-Essex County. “Our staff are working day and night to make sure that we have all the logistics of getting the swabs done.”
Once, when a promised shipment of swabs didn’t show up, the health unit had to delay testing a home as it scrambled to get supplies from its hospital partners, Ahmed said. He and other public health officials expressed dismay at the premier’s command to “start picking up your socks.”
“We have been continuously working every day for the last two months with no break, ensuring that our community gets what it needs. And so it was a little bit disappointing to feel that the premier thinks that way,” he said.
“We have been continuously working every day for the last two months with no break, ensuring that our community gets what it needs.” DR. WAJID AHMED ASSOCIATE MEDICAL OFFICER OF HEALTH FOR WINDSOR-ESSEX COUNTY